Volume 6, Issue 5, Pages 1219-1232 (November 2000) The Structure of Ribosome-Channel Complexes Engaged in Protein Translocation  Jean-François Ménétret, Andrea Neuhof, David Gene Morgan, Kathrin Plath, Michael Radermacher, Tom A Rapoport, Christopher W Akey  Molecular Cell  Volume 6, Issue 5, Pages 1219-1232 (November 2000) DOI: 10.1016/S1097-2765(00)00118-0

Figure 1 Isolation of Ribosome-Channel Complexes (A) Yeast ribosomes were mixed with proteoliposomes containing purified yeast Sec61p complex (Sec61p) or with liposomes lacking protein. The membranes were floated in a sucrose gradient and solubilized in digitonin, and the ribosomes were sedimented. Equivalent aliquots of the individual components, of the original mixtures (T, for total), and of the floated (F) and pellet (P) fractions were subjected to SDS-PAGE and analyzed by staining with Coomassie blue or by immunoblotting with antibodies to Sec61p. The asterisks indicate the positions of the three subunits of the Sec61p complex. (B) Radiolabeled 86mer of preprolactin (pPL86) was synthesized in a reticulocyte lysate in the presence of proteoliposomes containing canine Sec61p complex and SRP receptor. The membranes were floated in a sucrose gradient at either 100 or 500 mM salt and solubilized in digitonin at the appropriate salt concentration, and the ribosomes were sedimented. Equivalent aliquots of the original sample after translation (T), after flotation (F100 and F500) or after pelleting of the ribosomes (P100 and P500) were analyzed by SDS-PAGE followed by autoradiography. Each of the samples was also analyzed after precipitation with CTABr (CTABr-ppt). The percentage of CTABr-precipitable material is given below the lanes. (C) As in (B), except that liposomes without protein were used. (D) As in (B), except that ribosome-stripped native membranes (PK-RM) were used and flotation and solubilization were performed at 500 mM salt. All samples were analyzed by both CTABr precipitation and proteolysis with proteinase K (ProtK). The final pellet fraction was also incubated on ice for either 1 or 5 hr to test the stability of the ribosome-channel complex. Four times more material was loaded in F and P samples than in T samples. (E) As in (B), except that a nonprogrammed translation mix was used and the ribosomes in the original sample (T; 10% loaded) and in the final pellet fraction (P) were detected by immunoblotting with an antibody to the ribosomal protein S26. Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)

Figure 2 Ribosomes Associated with Purified Sec61p Complexes (A) The complex of yeast ribosome (green) and yeast channel (gold) lacking a nascent chain is viewed along the plane of the ER membrane (frontal view). The threshold level was chosen to encompass 100% of the ribosomal volume. The small (S) and large (L) ribosomal subunits are indicated. (B) The yeast complex is viewed from the ER lumen (bottom view). This view is generated by a 90° rotation about the horizontal axis, followed by a 90° rotation about the vertical axis in the plane. (C) A similar view as in (B), with the circumference of the yeast channel outlined in gold to reveal the nascent chain tunnel exit (TE). (D) The complex of rabbit ribosome (purple) and canine channel (gold), lacking a nascent chain, is shown in frontal view. (E) The mammalian complex lacking a nascent chain shown in bottom view. (F) The mammalian complex, lacking a nascent chain, is shown in frontal view with a threshold that encompasses approximately 150% of the expected ribosomal volume. (G) The complex of rabbit ribosome (purple) and canine channel (red), with the 86mer of preprolactin present, is shown in frontal view. (H) The mammalian complex with a nascent chain shown in bottom view. (I) The mammalian complex with a nascent chain is shown in frontal view with a threshold that encompasses approximately 150% of the expected ribosomal volume. Connections (c) between the channel and large subunit are indicated by arrows. Scale bar = 100 Å. The color code of the ribosomes and of the channels plus and minus nascent chain (NC) is shown as a vertical bar on the lower right. Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)

Figure 3 Ribosomes Associated with the Sec61p Complex Derived from Native Membranes (A) The complex of nontranslating rabbit ribosomes (purple) and canine channels (gold), which was derived from ribosome-stripped membranes (PK-RM), is viewed along the plane of the ER membrane (frontal view). The threshold level was chosen to encompass 100% of the ribosomal volume. The small (S) and large (L) ribosomal subunits are indicated. (B) The mammalian complex, derived from PK-RM, without a nascent chain is viewed from the ER lumen (bottom view). The threshold is at 100% ribosome volume. (C) As in (A), with a threshold that encompasses approximately 150% of the expected ribosomal volume. Connections (c) between the channel and large subunit are indicated by arrows. (D) The complex of rabbit ribosome (purple) and canine channel derived from PK-RM (red), with the 86mer of preprolactin present, is shown in frontal view. (E) The mammalian complex, derived from PK-RM, with a nascent chain present is shown in bottom view. The threshold is at 100% ribosome volume. (F) As in (D), with a threshold that encompasses approximately 150% of the expected ribosomal volume. (G) The complex of canine ribosomes (blue) and canine channels (red), derived from native high salt–washed ER membranes (K-RM), with endogenous nascent chains present, is shown in a frontal view. (H) The mammalian complex with endogenous nascent chains is shown in bottom view. (I) A similar view as in (H), with the circumference of the canine channel outlined in red to reveal the nascent-chain tunnel exit. The smaller hole is only a dimple. Scale bar = 100 Å. The color code of the ribosomes and of the channels plus and minus nascent chain (NC) is shown as a vertical bar on the lower right. Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)

Figure 4 A Gap between the Ribosome and the Channel (A) 3D structure of canine ribosome-channel complexes derived from native membranes. A mixed population of nascent chains is present. Shown is a frontal view at a threshold level corresponding to 150% of the ribosome volume. Arrows point to connections. Grey features indicate background noise. Scale bar = 100 Å. (B) Similar view as in (A), except that the threshold was chosen to give a ribosomal volume of approximately 200%. (C) A thin section is shown from the map, with the channel oriented at the bottom and the approximate position of the membrane (M) indicated. The map is contoured at three thresholds, corresponding to 100% (green), 150% (yellow), and approximately 200% (white). The gap and nascent chain exit tunnel (white dots) form a continuous path from the peptidyltransferase center (PTC) to the cytosol with a diameter of approximately 20 Å, even at a 200% threshold. Maps were displayed in “O” (Jones et al. 1991). (D) A view similar to that in (C), with two thresholds for the ribosome-channel complex, 100% (green) and approximately 200% (white). Superimposed on this view is a statistical map (in blue), which defines regions that are lacking positive electron density (>99% confidence interval) and may correspond to solvent. The tunnel is labeled “T.” (E) The bottom views of ribosomes from ten structures, including the first 6 listed in Table 1 and four other unpublished maps, were superimposed, and connections to the channel were identified. These connections are shown as gray regions within the outline of a semitransparent native channel (the numbers indicate how many structures contributed to a connection). The tunnel exit (TE) is indicated, and a possible lateral opening for the nascent chain is marked with an arrow. (F) A view similar to that in (E), with the connections overlayed in red onto high-density features (blue mesh) that surround the tunnel exit. The lines indicate the boundaries between the small (S) and large (L) ribosomal subunits. Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)

Figure 5 Interaction of Ribosomes with Membranes (A) Three images of yeast ribosomes associated with channels in vesicles are shown on the right (protein and lipid are white). A projection map of the final 3D reconstruction is shown on the left. The small (S) and large (L) ribosomal subunits are labeled, and the membrane is indicated (M). (B) Three images of canine ribosomes associated with channel complexes in native membranes (K-RM) are shown on the right. A projection map of the final 3D reconstruction is shown on the left. (C) A 3D surface for the yeast ribosome-vesicle map is shown in the frontal view. A gap is seen between the ribosome (green) and the membrane (gold). The double arrow gives the distance between a recognizable feature on the ribosome to the center of the membrane. (D) A bottom view of the yeast vesicle 3D map is shown at a higher threshold to reveal significant channel density over the nascent-chain exit tunnel. (E) For comparison, a frontal view of the solubilized yeast ribosome-channel structure is shown. Note that the length of the double arrow is similar to that in (C). Scale bar = 100 Å. Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)

Figure 6 Structure of the Translocation Channel (A) The purified canine Sec61p channel in the presence of the 86mer of preprolactin is viewed from the ER lumen at thresholds equivalent to 120%, 110%, and 100% of the associated ribosome volume. (B) The canine channel derived from native membranes in the presence of a mixed population of nascent chains is viewed from the ER lumen at a threshold series as in (A). (C) As in (A), but viewed from the side along the membrane plane. (D) As in (B), but viewed from the side along the membrane plane. The lumenal domain (LD) is indicated. (E) The purified canine Sec61p channel in the absence of a nascent chain is shown in gold as a wiremesh surface viewed from the ribosome (left panel). The center and right panels show slices through the channel. These slices correspond to a view along the shortest axis and a view offset by approximately 45°, respectively. (F) The canine channel in the presence of a mixed population of nascent chains is shown in orientations similar to those in (E). (G) An overlap view (center panel) of the two maps from the left panels in (E) and (F) is shown. The native channel is semitransparent, and the lumenal domain has been removed. The original maps are shown on either side. (H) An overlap view (center panel) of the two maps from the right-most panels in (E) and (F) are shown. The native channel is semitransparent. The original maps are shown on either side. Scale bar = 100 Å. Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)

Figure 7 A Lumenal Protrusion in Native Channels Formed Either by TRAP or OST (A) Pancreatic microsomes washed with high salt (K-RM) were extracted in digitonin without salt. This resulted in a supernatant (tot; 10 eq loaded) and a pellet fraction. The pellet was extracted first with a buffer containing digitonin and 0.5 M salt, which resulted in a supernatant (S0.5tot, 10 eq) and a pellet containing ribosomes and associated membrane proteins. To release the membrane proteins, the pellet was treated with puromycin in digitonin at 1.2 M salt. After centrifugation, a supernatant (Sptot, 50 eq) and a pellet (Pp, 5 pmol ribosomes loaded) were obtained. To enrich for membrane proteins, a portion of all supernatant fractions was extracted with Triton X-114, and the detergent phase was analyzed (S0TX-114 (20 eq), S0.5TX-114 (20 eq), SpTX-114 (100 eq). All samples were subjected to SDS-PAGE and analyzed by staining with Coomassie blue. Lanes 9–12 show purified canine ribosomes, Sec61p, OST, and TRAP complexes. Dots, triangles, and diamonds indicate subunits of the OST, Sec61p, and TRAP complexes, respectively. (B) Native membranes (K-RM) were extracted with digitonin at low salt concentrations to remove most lumenal proteins. The membranes were subjected to the usual procedure to generate ribosome-channel complexes, and their structure was determined. (C) Ribosome-stripped microsomes (PK-RM) were solubilized in deoxyBigCHAP at high salt concentration, and the extract was treated with hydrophobic beads to remove the detergent. The resulting proteoliposomes were incubated with nontranslating ribosomes and solubilized, and a structure was determined. Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)

Figure 8 Possible Pathways for the Nascent Chains of Secretory and Membrane Proteins (A) A thin section was generated from the 3D structure of the ribosome-channel complex derived from native canine membranes. Internal solid surfaces revealed by the front cutting plane are filled with blue. The channel is colored in red. The predicted position of the preprolactin 86mer that extends from the peptidyltransferase center (PTC) to the channel is indicated by a dotted line. The chain likely adopts a loop structure and is representative of early stages of translocation. The small (S) and large (L) ribosomal subunits are labeled, and the boundary between them is marked by a dashed line. (B) The possible path for secretory nascent chains from the PTC to the ER lumen is indicated. (C) The possible path of a nascent membrane protein is shown when a cytosolic domain is being synthesized following the integration of a TM segment into the membrane (M). Molecular Cell 2000 6, 1219-1232DOI: (10.1016/S1097-2765(00)00118-0)